Oh ....! John McWhorter really made a fool of himself talking to Michael Behe. He think Behe nailed it in Darwin's Black Box, and has a big problem with random mutations being responsible for skunks and okapis, etc. I recommend either sticking to linguistics or taking a few courses on evolution.

No wonder he asked the video to be taken down. No such luck, though: On Uncommon Descent, of course. They are loving it.

The Swedish newspaper that published an article by a freelance journalist claiming that Israeli troops harvested organs from Palestinians, is being sued. See previous post about the freedom of the press.

Attorney Guy Ophir filed a $7.5 million libel suit in New York on Tuesday against Aftonbladet, the Swedish tabloid that published the report Aug. 17. Ophir said the article's allegations were anti-Semitic and amounted to a "racist blood libel" against Jews.

The article as well as Aftonbladet's journalistic methods have been heavily criticized in Sweden, but the right to publish the article has been unanimously defended.

"Aftonbladet was within its rights to publish the article, and neither the Chancellor of Justice, nor the Israeli government, nor the Swedish ambassador has the right to interfere with that decision," wrote the editor-in-chief of [Expressen's, Aftonbladet's major tabloid rival] culture section, Björn Wiman.

Among the 1101 current signatories to Project Steve are 100% of eligible Nobel laureates (Steven Weinberg and Steven Chu), 100% of eligible members of President Obama's Cabinet (Steven Chu, the Secretary of Energy), at least ten members of the National Academy of Sciences, the authors of widely used textbooks such as Molecular Biology of the Gene, Psychology: An Evolutionary Approach, and Introduction to Organic Geochemistry, and the authors of popular science books such as A Brief History of Time, Why We Age, and Darwin's Ghost. When last surveyed in February 2006, 54% of the signatories work in the biological sciences proper; 61% work in related fields in the life sciences.

In an article in Scientific American, Depression's Evolutionary Roots, it is argued that depression is adaptive because it makes us think harder. Think about that for a moment.

Depression seems to pose an evolutionary paradox. Research in the US and other countries estimates that between 30 to 50 percent of people have met current psychiatric diagnostic criteria for major depressive disorder sometime in their lives. But the brain plays crucial roles in promoting survival and reproduction, so the pressures of evolution should have left our brains resistant to such high rates of malfunction.

Perhaps I think the current psychiatric criteria for major depressive disorders are rather liberal, but that's a different story. I'll accept that many people experience being really, really sad at some point in their lives.

Here's the link between depression and thinking:

One reason to suspect that depression is an adaptation, not a malfunction, comes from research into a molecule in the brain known as the 5HT1A receptor. The 5HT1A receptor binds to serotonin, another brain molecule that is highly implicated in depression and is the target of most current antidepressant medications. Rodents lacking this receptor show fewer depressive symptoms in response to stress, which suggests that it is somehow involved in promoting depression. When scientists have compared the composition of the functional part rat 5HT1A receptor to that of humans, it is 99 percent similar, which suggests that it is so important that natural selection has preserved it. The ability to “turn on” depression would seem to be important, then, not an accident.

(...)

Studies of depression in rats show that the 5HT1A receptor is involved in supplying neurons with the fuel they need to fire, as well as preventing them from breaking down. These important processes allow depressive rumination to continue uninterrupted with minimal neuronal damage, which may explain why the 5HT1A receptor is so evolutionarily important.

Okay, so 5HT1A promotes depression by binding to serotonin, but it also helps fueling neurons so we can think well. They therefore argue that depression is good for you, because you think better when you are depressed.

Of course, correlation alone is not enough to imply causation, and the authors do attempt to suggest a mechanism that would make sense of depression causing better thinking:

Many other symptoms of depression make sense in light of the idea that analysis must be uninterrupted. The desire for social isolation, for instance, helps the depressed person avoid situations that would require thinking about other things. Similarly, the inability to derive pleasure from sex or other activities prevents the depressed person from engaging in activities that could distract him or her from the problem. Even the loss of appetite often seen in depression could be viewed as promoting analysis because chewing and other oral activity interferes with the brain’s ability to process information.

Except that the two very things that usually make traits adaptive are precisely what are offered as damaging to thinking: sex and food. We are meant to believe that thinking about one's problems is so much more important than having sex and eating that having a depression is adaptive. That is one hell of a big mouthful that requires a few exclamation points.

Laboratory experiments indicate that depressed people are better at solving social dilemmas by better analysis of the costs and benefits of the different options that they might take.

In the meantime the rest of us will be over here having dinner and sex.

Here's how it's gonna go down: The brain is developmentally complex, with multiple proteins required to build each component, and proteins involved in building multiple components. Epistasis and pleiotropy, respectively, if you think of proteins as genes. The brain is not optimally designed, but has evolved using available proteins for new functions. It has had to make do with what was already present, at least in many cases, and that has resulted in some constraints that we now have to deal with. Such as being good at thinking analytically unfortunately comes at the cost of higher risk of being depressed, for example.

"Ever since Darwin"™ [1] it has been thought that the human vermiform appendix doesn't serve a function any more, but that the function was lost, and the remnant lingers on - something that is easily explained by evolution, but not so easily explained by creationism.

Then a research team from Duke University came along and changed all that.

First they demonstrated that the appendix does have a function [2]:

the human appendix is well suited as a “safe house” for commensal bacteria, providing support for bacterial growth and potentially facilitating re-inoculation of the colon in the event that the contents of the intestinal tract are purged following exposure to a pathogen.

Proposed function of appendix as providing support for growth of bacteria essential to the function of the intestine.

Then they show [3] that

Although the appendix has apparently been lost by numerous species, it has also been maintained for more than 80 million years in at least one clade, supporting the idea that the structure has a vital biological function.

Part of the phylogenetic tree showing that the appendix most likely evolved more than once (red, appendix present; gray, appendix absent). Note that this part of the tree doesn't show that the monotremes (platypus, echidna) and some marsupials also have something that looks like an appendix.

Both of these papers separately point to evidence that the human vermiform appendix is not a useless structure. The interpretation is not in question - no biologist do (should) not have any problem understanding the implication of this, namely that the status of the appendix has changed to one of use, but that while Darwin was wrong about this particular point, this conclusion in no way takes anything away from evolutionary theory as a whole. Creationists are guaranteed to jump out and imply that this means there is a problem with evolution, but it cannot be said with enough emphasis that it in no way means that. Again, evolution can explain such organs of no use, but creationism can't. That one structure is no longer considered neutral with respect to fitness does not mean that such neutral organs don't exist. Examples:

leg bones in whales

eyes of blind cavefish

pelvis remnants in snakes

the human tailbone

human goose bumps

human muscles to move the ears (I'm very skilled at this myself)

There are many more. Some of these may one day, like the human appendix, be demonstrated to have a function (i.e. increase fitness), but it is highly doubtful (it is unthinkable) that the status will change for all of them.

A question of semantics

What do we call such organs/structures/behaviors that no longer serve any function? If we distinguish between those that used to have one function but now has another (penguin wings, for example) and those that used to have a function, but now doesn't at all (see list above), then I personally find it most useful to call only the latter vestigial. However, some people use the term in both cases (Jerry Coyne is said to do so in Why Evolution Is True, for example), but I find it more informative to call the former structure exapted, preadapted, or co-opted (I use co-opted, because the first to are usually used a nouns, exaptation and preadaptation - and that reminds me that Todd Oakley still owes me to explain what the difference between these three are).

So, I'll say that the human appendix is not a vestigial organ.

A question of politics

All of the above is really fairly straightforward (but exciting) science discourse. However, our own PZ Myers has reacted rather strongly in a post, Darwin and the vermiform appendix.

Before I go on, let me make a few things clear before anyone says otherwise: PZ is a great blogger, when blogging about science as well as about creationism and all things related to either one. I happen to be fairly aligned with him in terms of politics as well as on religion (we are both atheists), and I agree with him on most issues that he brings up on his blog. Notably, I side with him on the question of "Crackergate," "Expelled from Expelled," and share his disdain for the faitheists, just to name a few.

The post from today about the human appendix paper is the first example where I strongly disagree with PZ. He doesn't so much talk about the scientific paper itself, but instead about an article in ScienceDaily, Evolution Of The Human Appendix: A Biological 'Remnant' No More, in which we are introduced to the evolutionary significance of the study:

Now, some of those same researchers are back, reporting on the first-ever study of the appendix through the ages. Writing in the Journal of Evolutionary Biology, Duke scientists and collaborators from the University of Arizona and Arizona State University conclude that Charles Darwin was wrong: The appendix is a whole lot more than an evolutionary remnant. Not only does it appear in nature much more frequently than previously acknowledged, but it has been around much longer than anyone had suspected.

"Maybe it's time to correct the textbooks," says William Parker, Ph.D., assistant professor of surgical sciences at Duke and the senior author of the study. "Many biology texts today still refer to the appendix as a 'vestigial organ.'"

[Emphases added.]

Parker then said

Darwin simply didn't have access to the information we have. If Darwin had been aware of the species that have an appendix attached to a large cecum, and if he had known about the widespread nature of the appendix, he probably would not have thought of the appendix as a vestige of evolution.

He also was not aware that appendicitis, or inflammation of the appendix, is not due to a faulty appendix, but rather due to cultural changes associated with industrialized society and improved sanitation. Those changes left our immune systems with too little work and too much time their hands – a recipe for trouble.

That notion wasn't proposed until the early 1900's, and we didn't really have a good understanding of that principle until the mid 1980's. Even more importantly, Darwin had no way of knowing that the function of the appendix could be rendered obsolete by cultural changes that included widespread use of sewer systems and clean drinking water.

Here is, then, the relevant passage from Darwin [1]:

Not only is [the vermiform appendage of the caecum] useless, but it is sometimes the cause of death

[Emphasis added.]

He doesn't use the term vestigial, but instead is very careful (I gather) to say that it no longer has any use (in fact, it isn't even just neutral, per Darwin's observation, but detrimental).

Here are a few quotes from PZ's post about the ScienceDaily article, and my answers to each of them:

It's rather unseemly to collect a lot of data that Darwin did not have, run it through PAUP 4.0 on a fast computer, map the data onto a molecular consensus phylogeny, and cackle gleefully over discovering something Darwin did not know. Really, it doesn't make you a better scientist than Darwin.

"Cackle gleefully" ? Who, Parker? "Make you a better scientist" ? Where does this come from? Parker isn't implying any such thing.

To make it even worse, people who do this can't even make the corpse-fight a fair fight — they have to stuff the pathetic dead body with straw. In this case, they're padding Darwin's investment in the appendix a fair amount. They cite one work by Darwin, The Descent of Man, which mentions this issue. He wrote one whole paragraph on the topic, and here it is, in its entirety;

Go to PZ's post to see the quote, which includes the sentence I quote from Darwin above, where he labels the appendix as 'useless.' People criticize the work of dead scientists on scientific grounds as a matter of routine. There is absolutely nothing wrong with it. Indeed, this is the way things must be, in order for science to progress. PZ would agree, I know, and I am puzzled why he would scold Parker in this manner.

Note why Darwin classed this appendage as vestigial: because it is greatly reduced compared to the homologous organs in non-human relatives, and because it currently exhibits a great range of variation, which is apparently non-functional. These are criteria which the paper in question does not refute at all. Darwin does say that the appendix is "useless", and the paper will show some evidence that that is wrong. It's also irrelevant.

The reason why it is irrelevant is that the presence of some function is not part of the definition of a vestigial or rudimentary organ

It is not relevant that the appendix is useless? The hell?! PZ harps about the semantics - vestigial vs. useless - but then ignores the meaning behind Parkers's words. Parker clearly means 'useless' when he says 'vestige'. Of that there can be no doubt. How can it be irrelevant whether the appendix has a use, when that is what both papers are all about? (It can't, and it isn't.)

If a portion of the gut, a digestive organ, is diminished in size such that it no longer contributes to the primary function of the organ, but does retain a secondary function, such as assisting in immunity, or as the authors of the recent paper will argue, in acting as a reservoir of bacteria for recolonizing the gut, then it is still a vestigial organ. It has lost much of its ancestral function.

PZ is using one definition of the word, and not the other (see semantics above).

I mentioned that I'd point out errors in Darwin's understanding. They're there, but note that seeing them now 150 years after he wrote his big book does not make me smarter than Darwin, nor does it invalidate the overall picture of his theory.

And Parker neither said nor implied anything to that effect. In fact, he goes to great length to emphasize that "Darwin simply didn't have access to the information we have," and "If Darwin had been aware of the species that have an appendix attached to a large cecum, and if he had known about the widespread nature of the appendix, he probably would not have thought of the appendix as a vestige of evolution." That, and the rest of the Parker's words above from the ScienceDaily article.

Most of my complaints here are with the abysmal presentation of the ideas in it by the popular press, aided and abetted by the scientists themselves. Just keep in mind that whenever these press releases that declare "Darwin was wrong" appear, it's usually an example of grandstanding and the regrettable tendency of competitive scientists to think the way to impress people with the importance of their work is to get into a penis-measuring contest with poor dead Chuck.

I was very careful to put "Darwin was wrong" in the title of this post. This is the "abysmal presentation" that PZ is referring to. PZ co-authored a letter to the New Scientist, when they printed those exact words in big letters on the cover of the January 2009 issue. (That cover story was about the uprooting the tree of life, and how parts of it isn't at all like a tree, but a network. I agree it was foolish to choose that headline for the cover, but, luckily, as things have turned out, it didn't really have much of an effect as far as I have seen.) I also think it is impressive when scientists can finally prove Darwin wrong on something. If no one else have been able to do it for almost 150 years, then let us indeed celebrate it with much fanfare whenever someone can. Darwin would have been proud.

I think PZ has got the heebie-jeebies. He is at the forefront of defending evolution against creationist imbeciles, so it is understandable that he dislikes it when scientists gives them ammo for their cannons (note to self: find a better idiom). However, when communicating science, we should not be hesitant to say things the way they are, and in this case "Darwin was wrong: The appendix is a whole lot more than an evolutionary remnant." Trying to boost your scientific work in the popular media by such statements is fair game. It's very hard to get people interested, and I personally applaud Parker for the way he did it, and for standing up for "poor dead Chuck" at the same time. Yeah!

Lastly, let me briefly say how disagreeable I find the discourse in the comments to many of PZ's posts, this one in particular. People call each other names for voicing opinions not shared by the majority of the commenters. Accusing them of trolling is standard practice, akin to shouting 'witch' back in the middle ages, and one is a 'fucktard' when they don't like you. But worse than that, ScienceBlogs is a place for science bloggers, and the number one trait of a good scientist is skepticism. Pharyngulites as a group don't have too much of it; commenting how much they are in agreement with PZ on whatever he writes about, spiced with sublime derogatory terms, seems to be a hobby of hundreds of regular visitors. A few quotes from comments to the post in question:

"some idjits think that makes the whole work of the innovator wrong.""As Prof. Myers points out, Darwin was wrong about a lot of things. So what?""Picking a fight with Darwin over it is just stupid.""So, basically, they didn't understand what Darwin meant by "vestigial" because they didn't do all their homework."

It's not all bad, though. Here's one dissenting voice: "If we are to refer to all homologous structures with different functions as vestigial, it seems to have become a useless term."

Exactly my point.

References:

[1] Darwin, C. 1871. The Descent of Man and Selection in Relation to Sex.

Israeli Foreign Minister Avigdor Lieberman doesn't seem to understand what it means to have a free press. Just like the days when the Danish Prime Minister was asked to censor Jyllands-Posten for publishing the drawings on Muhammad, now, despite Lieberman's request, Sweden's Foreign Ministry is refusing to condemn an article (CNN, BBC, Politiken) published in a Swedish newspaper, Aftonbladet, in which Israeli troops are accused of harvesting organs from dead Palestinians (original article in Swedish).

"It's a shame that after the Swedish ambassador to Israel did the right thing and condemned the report, clarifying that this newspaper does not represent Sweden in any way or form, the Swedish Foreign Ministry chose to dismiss her statement instead of supporting it," Lieberman said.

"The meaning of freedom of press is the freedom to publish the truth, not the freedom to lie and slander. A country which really wants to defend democratic values must strongly condemn false reports that reek of anti-Semitism like the one published this week by the Aftonbladet newspaper."

The free press in Scandinavia is really free. Without fear of government intervention of any kind, they really can write whatever they want. Private parties can sue them for libel, but the government is never involved. I find it ironic that Lieberman here thinks he is in any position to tell the Swedes what it means to have a free press. As for his insinuation that the article is not the truth, it is baffling that he suggests that the Swedish government should believe his word on the matter, without any prior assessment of the facts.

The free-lance author of the op-ed article (need i say 'of course') received threats on his life:

"I have an e-mail here ... saying, 'The Nazis should die and you will be next. We will meet you outside, you will be the next news very soon. Meet you outside,' " Bostrom said.

Just to be fair and balanced I am now looking for death threats made by Danish and Swedish citizens against other nationals writing articles criticizing anything Danish or Swedish, or drawing indecent cartoons of Jesus or our royalty (actually, Danish people take pride in doing just that themselves - see below).

Here's a Turkish drawing from 2005 of then Danish prime minister Fogh Rasmussen in bed with Kurdish leader Abdullah Öcalan. Fogh Rasmussen said his honor had been challenged, and then ordered a nuclear attack on Ankara.

Oh wait. Strike that. It says he just shook his head a bit and laughed about it.

Jesus!

Queen Margrethe (center, smoking, as usual).

Danish roligan stops evolution? Looks like Fogh Rasmussen third from the left. That's probably not a coincidence.

Here's a story reminiscent of the ruckus caused by (the reaction to the) Danish cartoons of Muhammad back in 2005.

(Some) Hindus are crazy like the rest of them. An Indian artist depicted Ganesh, god of intellect and wisdom (among other things), performing a Maori dance, walking naked carrying a garden rake, and in the pose of Auguste Rodin’s The Thinker. As a result he was received threats on his life and on his fingers.

The artist added that the threats began when Sanatan Sanstha, a hard-line group which presents Hinduism as a form of science, told Hindus to call him and “express their anguish” at the images.

As a form a science. Right. If you're that far out it's no wonder a depiction of your beloved god will make you threaten someone on their life. (No, I am not saying I would ever threaten anyone because they dissed Issac or Charles.)

One, the extremist organisation Hindu Janagruti Samiti (HJS), called for demonstrations at the exhibition venue.

“We intend to have peaceful protests, but we are not responsible for any law and order problem if it arises,” said Jayesg Thali, an HJS convener.

Oh, and we were so worried, but this of course makes it completely safe! No instigation of religious mobs with hurt feelings going nuts can be imagined now.

Hokkaido University in Japan have an advertisement in Nature (July 9th, 2009) where they invite Ph.D.s to apply for faculty positions. They will hire 25 professors (assistant/associate) and lecturers over the next five years for science, technology, and agriculture positions. "Applications are open only for female researchers." (original emphasis)

Ultimately, who are hired in faculty positions should only be based on merit. The best candidates should be hired, giving no consideration to gender, species, race, height, religion, food preference, martial status, sexual preference, vertigo, et cetera, et cetera, given that none of these would interfere with job function. It therefore seems unfair that Hokkaido University will earmark positions for females, when there might be better qualified males who would have liked to apply.

However, society (Japan in particular) is already heavily biased in terms on merits. Women do not have the same opportunities as men for at least two different reasons.

1. Role models. It will become much more likely that other women will find becoming a professor a reachable goal once they see others achieving it. We may not think that this should be the case - after all the whole point is that gender doesn't matter, but that only qualifications do - but the fact is that it does. Who we identify with is demonstratively influenced by the characteristics that we share.

2. Remedying Discrimination. Women has a tough time being hired as professors in Japan, probably for several reasons. I recall reading that a female applicant was turned down because a male applicant "needed the job to provide for his family, while the female applicant had her husband to do that." (Paraphrasing from memory.) Additionally, the reason that there are fewer female professors do of course have something to do with there being fewer qualified female candidates, but that is most likely because fewer women see that path as one that is viable for them, in part because there is a bias in what students are encouraged to pursue in the educational system (boys do math, girls do language, or some such stereotype). Discrimination continues to exist in the favor of males for hiring professors, and to remedy that, tipping the scale in favor of women will arguably have a positive effect.

For more information on the positions at HU go to F3 project: fortississimo affirmative action in Hokkaido University. (It's only in Japanese, so it appears application is also open only for Japanese speakers?)

P.S. A couple of places here I have made some assertions that I believe to be true. I have read, for example, that who we identify with influences our career choice, and that we identify with those who are similar to. Forgive me for not listing references, but I trust the enthusiastic reader will have no problems locating sources that argue this and other points.

Abdel Basset Ali al-Megrahi, the only person convicted in the 1988 Lockerbie jet bombing, has been released from prison in Scotland because he is expected to die soon from prostate cancer. You can think what you want about that (and I think it's crazy), but the thing I really want to object to is the reception he got when he returned to Libya (see picture).

Ignoring American demands that Mr. Megrahi not be celebrated as a hero returning to his homeland, hundreds of young Libyans were bused to the military airport in Tripoli to welcome him home, cheering and waving Libyan and Scottish flags as he sped off in a convoy of white vehicles.

Very interesting experiment is blogged on 80beats of the Discover Magazine, To Win the Evolutionary Race, Robots Learn to Deceive. Brains of real robots were subjected to evolution, and the result was that they learned how to horde the most food for themselves, doing what they could not to attract other robots to the food, so they could have more for themselves.

On Tuesday, November 13, 2007, Sonny Perdue, the Governor of Georgia, led a group of approximately 250 persons, including many state officials, in a prayer for rain on the steps of the state capitol in Atlanta.1 Georgia had been suffering an extreme drought, and the level of Lake Lanier, an important water reservoir near Atlanta, had been decreasing dramatically over several months. Governor Perdue believed that a divine intervention was necessary and so he boldly asked God to bring rain.

It rained. The author, Gary J. Whittenberger, compares the amount of rain before and after the prayer with rainfall in the previous ten years to show that it wasn't an unusual increase in rainfall, especially considering that the prayer was done during a time of drought. As Allan Donald comments, regression to the mean explains the increase in rain all by itself.

Interestingly, several readers belittle the article, saying that it is ridiculous to even discuss the idea of praying for rain, that if people want to believe in the power of prayer, then you should just let them (note this is the Skeptic Magazine!), and that it’s silly and counterproductive to spend time "on an analysis that the author knew ahead of time couldn’t prove anything." The last remark I find quite true. There is no way that even a torrent of water the minute the prayer was over could convince me that the prayer was resposible, as long as there are other and better hypotheses. However, apparently, for the citizens of Georgia, less would suffice.

Many Georgians considered Perdue a hero and thought that his prayer had influenced God to increase rainfall to the drought stricken vicinity of Atlanta.

And therefore I think this article is not such a bad idea after all. Let the Georgians read it, and perhaps some of them will realize that the increase in rainfall coinciding with the prayer does not need to be an act of God.

Great article in the NY Times by Nicholas Wade on why humans have become (mostly) hairless: Why Humans and Their Fur Parted Ways. He quickly mentions the aquatic ape theory, but (rightly) leaves it at that. While some people are very much into the theory, certain isotopes would have been present in bones if humans had gone through an aquatic stage are absent (I can't find a reference for this at the moment, so instead take a look at other objections on Wikipedia). The hypothesis discussed is that loss of hair was adaptive because of fleas, which were highly beneficial to get rid of.

David Sloan Wilson discusses the evolution of war with John Horgan, Evolution and War: Basic and Advanced. Wilson said Horgan flunked Evolution 101, and Horgan then called Wilson arrogant. Wilson then takes a deep breath.

Gary Ruvkun: “My rule of thumb is to ignore the evolutionary biologists — they’re constantly telling you what you can’t think.” Again Nicholas Wade in the NY Times, Tests Begin on Drugs That May Slow Aging.

Homo floresiensis (nicknamed "the hobbit") is the name given to a hominin species whose remains were discovered in 2004 on the island of Flores, Indonesia. But do the bones represent a new species at all, or were they, mundanely, anatomically modern humans with some pathological disorder that caused them to have smaller brains (~400 cc) and be shorter (106 cm) than humans (~1130 cc and 147 cm, average for women and Indonesian women, respectively)?

I have previously made clear where I stand in that debate, and for what reasons, but at the same time I do have some reservations with a paper in the Journal of Human Evolution that applies cladistic analysis (also known as phylogenetics) to determine where in hominin evolution H. floresiensis fits in.

The authors, Argue et al., examined multiple morphological features of bones of H. floresiensis, H. ergaster, H. erectus, H. habilis, H. rudolfensis, A. africanus, A. afarensis, H. rhodesiensis, H. georgicus, and H. sapiens in order to compare them and construct cladograms (evolutionary or phylogenetic trees showing ancestral relationships). Because some scientists suggest that the smaller brain case could have been caused by microencephaly, they excluded cranial capacity from the comparisons.

The result is that two trees are the most parsimonious, meaning that they are the shortest of all the trees they examined. In other words, under the assumption that the fewer morphological changes between the species is the better model for the evolutionary relationship, these two trees are the most likely of all.

The two most parsimonious cladograms, with H. floresiensis branching off just after and just before H. habilis, respectively. Dmanisi is also known as Homo georgicus.

So the conclusion the authors make seems fair enough: H. floresiensis branched off either just after or just before H. habilis.

Skipping over the problems I have with the assumption of parsimony, does anyone else notice something really fishy so far?

The fishy part is that in order to construct cladograms like the ones above, the authors assumed that H. floresiensis and H. sapiens are different species. Once that is done, no other conclusion can be reached. It is perhaps interesting by itself to see what the evolutionary relationship is between them, assuming that they have one, but it can't address the question of whether they are different species or not. However, Argue et al. state clearly in their introduction that this is their goal:

Alternative interpretations include the possibility that the Liang Bua fossils represent a new hominin species, H. floresiensis (...), and that the holotype specimen, LB1, was a modern human, possibly afflicted with a pathological condition (...). These conflicting hypotheses are based on comparative analyses of the morphology of the bones with both archaic and modern Homo, typically using statistical methods to compare the Liang Bua bones with those of other hominins. The morphological and morphometric analyses have contributed much to the debate about H. floresiensis, but have not conclusively resolved the controversy about the position of the species in human evolution. We, therefore, use a different tool, cladistic analysis, which has not yet been applied to resolving this problem.

Again, I do not see how using cladistic analysis can be used to resolve this question of whether H. floresiensis was a human with a pathological condition or a separate species. In fact, the same issue exists between H. georgicus (Dmanisi) and H. erectus. H. georgicus is now thought to represent an early stage before H. erectus, rather than being a separate species. Yet, here they are assumed to be different species.

From their conclusion:

Based on rigorous cladistic analyses, we propose that H. floresiensis evolved in the Late Pliocene or Early Pleistocene. The first of our two equally parsimonious trees suggests that H. floresiensis branched after H. rudolfensis (represented by KNM-ER 1470) but prior to the divergence of H. habilis (represented by KNM-ER 1813 and OH 24). Alternatively, our results are equally supportive of H. floresiensis branching after the emergence of H. habilis.

Agreed. I too believe H. floresiensis to be a new species, and given that, I can accept the cladistic analysis (again, ignoring my issues with parsimony in cladistics).

In their earlier paper (Argue et al., 2006) the morphological data were used to support this conclusion, but, again, the results in the present paper does not "sustain H. floresiensis as a new species (...) and favor the hypothesis that H. floresiensis descended from an early species of Homo," when it is assumed that they are separate species.

Alan Turing was the greatest computer scientist ever born in Britain. He laid the foundations of computing, helped break the Nazi Enigma code and told us how to tell whether a machine could think.

He was also gay. He was prosecuted for being gay, chemically castrated as a 'cure', and took his own life, aged 41.

The British Government should apologize to Alan Turing for his treatment and recognize that his work created much of the world we live in and saved us from Nazi Germany. And an apology would recognize the tragic consequences of prejudice that ended this man's life and career.

There is much reason to be critical of the field of evolutionary psychology, not because it isn't obvious at some level that the human mind is an evolved organ, but rather because much of the research comes down to evolutionary just-so explanations of otherwise interesting studies of human psychology. When, on the other hand, this process is reversed, it does have scientific merit. The right way to do it is to start hypothesizing based on our evolutionary history, and then set forth to do experiments that may reject or validate these hypotheses.

An example of that is a study of the effects of bottle feeding. Based on what we know of our evolutionary history, the only reason that a new mother would prematurely cease breastfeeding her infant would be in the case of the infant's death. Bottle feeding had not yet been invented. Consequently, a team of scientists at the Department of Psychology, State University of New York in Albany surmised that bottle feeding mimics this loss, and that mothers who breastfeed would be more likely than average to experience postpartum depression.

The researchers found this hypothesis to hold true in a study of 50 new mothers:

We recently completed a study of over 50 mothers recruited through local pediatric offices at 4–6 weeks postpartum [25]. Consistent with previous reports, we found that those who bottle fed their babies scored significantly higher on the Edinburgh Postnatal Depression Scale than those engaged in breastfeeding. The increased risk of depression among mothers who relied on bottle feeding held true even after we controlled for such things as age, education, income, and the mother’s relationship with her current partner.

The authors don't label their study as evolutionary psychology, but as evolutionary medicine, and I commend the emergence of this new discipline. What can it bring to the table, then? The authors conclude that

Bottle feeding practices and hospital procedures that simulate child loss may increase the risk of postpartum depression and fall within a growing number of medical issues that could benefit from an evolutionary perspective.

[The paper is published in a journal owned by Elsevier, and is not free. If you want a copy of the PDF, let me know and I will send you one.]

How do we decide who we trust? When someone writes an article telling a mean story about someone else, how are we to know if this is the truth?

FIJI Water is doing very well, in part by promoting itself as Carbon negative, by boasting of various good deeds (e.g. permanently protecting a UNESCO World Heritage site and its rain forest from logging), and by being consumed by many famous people, such as Obama, Paris Hilton, and Mary J. Blige. At the same time the water really comes from Fiji, which is ruled by a military junta, and where many people ironically don't have access to clean water.

If you drink bottled water, you've probably drunk Fiji. Or wanted to. Even though it's shipped from the opposite end of the globe, even though it retails for nearly three times as much as your basic supermarket water, Fiji is now America's leading imported water, beating out Evian. It has spent millions pushing not only the seemingly life-changing properties of the product itself, but also the company's green cred and its charity work. Put all that together in an iconic bottle emblazoned with a cheerful hibiscus, and everybody, from the Obamas to Paris and Nicole to Diddy and Kimora, is seen sipping Fiji.

Nowhere in Fiji Water's glossy marketing materials will you find reference to the typhoid outbreaks that plague Fijians because of the island's faulty water supplies; the corporate entities that Fiji Water has—despite the owners' talk of financial transparency—set up in tax havens like the Cayman Islands and Luxembourg; or the fact that its signature bottle is made from Chinese plastic in a diesel-fueled plant and hauled thousands of miles to its ecoconscious consumers. And, of course, you won't find mention of the military junta for which Fiji Water is a major source of global recognition and legitimacy. (Gilmour [the company's founder] has described the square bottles as "little ambassadors" for the poverty-stricken nation.)

It's not that I have seen Lynda Resnick (current owner of FIJI Water) excoriate Anna Lenzer's claims, but I'll be damned if FIJI Water is willing to admit that they are true. Assuming that someone financially involved in FIJI Water will eventually answer (and by 'answer' I mean 'deny') part of her criticisms, my question is how it is that we'll believe one or the other.

I don't drink FIJI Water, though I'm sure it's tasty. Since recently I don't drink any bottled water, actually, but that's a different story (though not entirely). But if I was a long-time consumer of FIJI Water, I can see that the emotional investment that I had made would make me more likely to dismiss claim's such as Lenzer's, until I saw solid proof. (By 'emotional investment' I mean the fact that while drinking it regularly, I would expect that doing so wouldn't cause all sorts of calamities in another country, for example, and if I then had to admit to myself that I had been wrong all that time, then I would be emotionally upset - we don't like when that happens.) On the other hand, now that I don't drink it, I don't really have anything at stake, and I don't have to face the fact that I am part of the problem (that FIJI Water causes disease, climate change and other human and environmental tragedy).

But if reading just one article that highlights good reasons why we shouldn't be drinking it isn't enough to rationally make up our minds on the subject, then what exactly is enough? Two considerations, I would say:

1. Consider that history shows that those who stand to make or lose a lot of money are usually the ones who are fine with screwing over other people. This is to be contrasted with what history tells us about investigative reporters' practice of making up complete falsehoods just to get a great story printed.

Incidentally, I went to Ontario Mills Mall this sunday, and almost every vendor the food court were aggressively pushing FIJI Water - at $2.99 per pint. I asked around and was told that the decision to do so comes from the Manager of HMS Host, whom I now intend to write a letter of complaint to.

Important update 8/17:FIJI Water already had published a reply to Lenzer's article, and Lenzer has a reply to that on the same page. Bottom line is that while FIJI Water does do some charity work in the local Fiji communities, this does not excuse doing business with a dictatorship.

ResearchBlogging.org is a great site for the latest research in the natural sciences. Here bloggers apply to register, and then when they blog about peer-reviewed academic research on their own blogs, they import and get a link with a blurb on the site.

It's about how a group of people imagining how it would be to live in a society where sex is not permitted, and how that affects the participants attitudes towards people who are homosexual. It turns out that

"[people who was in this experiment] were more able to take the perspective of homosexuals, than were the control participants [who attended a lecture on homophobia] , and this in turn was associated with more empathy towards people who are homosexual, a greater tendency to think of homosexuals and heterosexuals as all belonging to the same category (being human) and ultimately to more positive attitudes towards people who are homosexual."

Unscientific America by Chris Mooney and Sheryl Kirshenbaum has been a hot topic in this realm of the blogosphere, but I haven't commented on it yet (since I have not and will not read it), leaving that to PZ and Coyne, whom I largely agree with on the issue (of whether to be a faitheist or a confrontationalist on the subject of compatibility between religion and science).

In an op-ed article today in the LA Times, Must science declare a holy war on religion?, they ask who is going to read Richard Dawkin's new book The Greatest Show on Earth (to be released this September) in which he makes the case for evolution. Their answer:

Surely not those who need it most: America's anti-evolutionists. These religious adherents often view science itself as an assault on their faith and doggedly refuse to accept evolution because they fear it so utterly denies God that it will lead them, and their children, straight into a world of moral depravity and meaninglessness. An in-your-face atheist touting evolution, like Dawkins, is probably the last messenger they'll heed.

But but but. While I would also guess that those who are firmly set in their religious beliefs and tenaciously anti-science aren't going to touch the book, those aren't the only audience that would benefit from reading it (in the eyes of pro-science folks). The people I hope will read it - as I know some have read The God Delusion - are younger people (teenagers, people in their twenties) who are perhaps fence-sitters, or even already totally pro-science, and these people will talk about it. Most won't know much about evolution at first, but with a book like this they will understand evolution better, be better able to have a conversation on the subject, and will talk about it with their friends, some of whom might be children of those very religious parents who would never read it. Perhaps they will start question the creation myth they hear in church, and stop accepting it on faith, as a result of reading a conflicting account.

The point is that these things take time. We won't persuade everyone in one fell swoop that evolution is true, but the more books out there, and articles on the internet, and public debates, and TV-shows, the higher the chance that the next generations will grow up being a little more skeptical than their parents, feeling some discomfort in having to read the Bible literally, and becoming more and more pro-science as a result.

Mooney and Kirshenbaum then invoke Darwin as an example of how they think the "New Atheists" should behave:

It turns out that late in life, when an atheist author asked permission to dedicate a book to Darwin, the great scientist wrote back his apologies and declined. For as Darwin put it, "Though I am a strong advocate for free thought on all subjects, yet it appears to me (whether rightly or wrongly) that direct arguments against Christianity & theism produce hardly any effect on the public; & freedom of thought is best promoted by the gradual illumination of men's minds, which follows from the advance of science."

Except that Darwin lived in a different time, where it might have been true that "direct arguments" had next to no effect (I am not sure of that either - just because Darwin said it doesn't make it so), but this is a different era, with mass communication and massive communication: while TV and radio aren't the media seething most with this controversy, the internet is constantly buzzing with it, and it is easy for anyone with internet access to find. Perhaps Darwin would have changed his statement had he known?

On the website of the Institute for Ethics & Emerging Technologies (or is that the Institute for Emerging Ethics & Technologies?), Mike Treder writes about the similar approach to turning rationality on and off when it suits your purpose: Creationism, Birtherism, Singularitarianism, and Other Fantasies. The last of the four are the climate change denialists, but he could easily have included the HIV denialists and the moon landing denialists. The connection between them all is that they are entire movements that purports to be in the business of discovering the facts, exposing conspiracies, enlightening the uninformed, and telling the truth. But, as Treder argues, a deeper, emotional, ideological force drives them to so fervently espouse their beliefs even in the face of contradicting evidence.

But! Before we laugh too hard in their faces, consider that this is something we all do on occasion. We are not Vulcans, and we all believe in big or small things that we don't often ourselves realize aren't based on anything but wishful thinking. I have several times as an adult come to learn that something I have believed about the World since I was a child simply isn't true. It can be hard to let go of beliefs that we have cherished (and indeed thought were based on evidence), but it can also be a joy to uncover them, if you can embrace such changes. Perhaps learning not to take yourself too seriously is a step in the right direction, rather than buying into an idea without having an exit strategy. </paternal mode>

Finally, a request. If you support science and reason, if you appreciate all that technology and secular society have done to relieve suffering, promote freedom, and bring opportunity to many, then please stick with your rationality even when it takes you to uncomfortable places. Don’t allow fear to overcome logic. Accept the facts and the truth even if they require you to change your opinions. In the long run, both you and the world we live in will be much better for it.

After reading yet another email from Human Events - Headquarters of the Conservative Underground (which I emphasize because the phrase is utterly ridiculable) - about the demands for Obama's birth certificate, I have now decided that the "birther" movement is a great thing for this country.

It is not a waste of anybody's time or resources, because the only people wasting their time on it are crazy conservative fundies who don't have anything valuable to contribute to this society anyway. So let them keep insisting that Obama produces his 1961 copy of his birth certificate - if he even has it!!! For the rest of us (i.e. who aren't self-proclaimed crazy conservative fundies) it needn't amount to anything but an occasional chuckle in the company of Keith Olbermann or Jon Stewart (and go to FactCheck.org to see the certificate).

Here are some of the better goodies in the incredible long conspiracy-theory style letter that I got this morning:

Soon, we will win. But we need YOUR help to get over that finish line!

Actually, we're still at the ridicule stage.

WHAT is Barack Obama trying to hide? WHAT is he afraid of? WHY doesn't he just release these documents to prove that he is a natural-born citizen and, therefore, qualified to serve as President -- especially his actual birth certificate?

It's a common tactic also of creationists to ask what their opponents are afraid of. "Why don't you show us the evidence that we evolved from monkeys? What are you afraid of?"

Frankly, the evidence that Barack Hussein Obama was born in Africa -- not Hawaii as he claims -- and, therefore, cannot serve as the President of the United States, is compelling.

Really? Let's see what this "compelling" evidence is (with my comments in red):

* First, Mr. Obama's refusal to release his birth certificate. If he has nothing to hide, what does he gain by refusing to allow the press to see the birth certificate? [The press has seen it.]* Second, the contention by Barack Obama's half-sister, Maya Soetoro-Ng, that Mr. Obama was born in a particular Hawaiian hospital, only to claim that it was in a different hospital several years later. Plus, there is the recent letter that Mr. Obama wrote, contradicting his previous statements as to which hospital that he claims to have been born in, in Hawaii. [So his sister can't remember an event she wasn't present at (she was born in 1970).]* Third, the erecting of a wall around Barack Obama's grandmother, the late Madelyn Dunham, by Mr. Obama, thus cutting off access to the one person then alive who would have been present if he was actually born in Hawaii. [Perhaps there was another reason to protect her against hordes of crazy conservative fundies late in her life? Either way, do you think there's a chance she would do anything but confirm that Obama was born in Hawaii?]* Fourth, the posting of law enforcement personnel at the two hospitals in Honolulu mentioned by Ms. Soetoro-Ng in an effort to block the press from discovering the truth about the birth certificate. [Or to control hordes of crazy conservative fundies, maybe?]* Fifth, a taped phone conversation with Mr. Obama's step-grandmother, who claims that she was present at his birth... in what is now called Kenya! [That would indeed be an interesting recording to listen to. I honestly never heard about it before. Let's hear it. Then weigh that evidence against all the people who testify that he was born in Hawaii. But, throwing the crazy conservative fundies a bone, do go searching for this taped phone conversation. Do spend all your time following this lead, please.]* Sixth, the "birth certificate" posted on the Obama campaign website and other liberal websites. Since Barack Obama was born in 1961, long before laser printers and office computers, his original birth certificate would be typewritten ... unlike the laser printed "copy" purported to be genuine. [As is very common, the birth certificate we have seen is not an original from 1961. The records of his birth are kept by the State of Hawaii, and they can print new copies on request. If Obama forged this certificate, that would be a felony committed years prior to running for for president (to get his passport, for example).]

So, reader, how "compelling" do you find this evidence? On a scale from -3 to 11, I'd say it's an imaginary number, like -666i.

Are you willing to see the Constitution shredded by the Left? Will you sit back and do nothing while a foreign-born person may be illegally occupying the White House as President of the United States?

I thought they wanted to just see the evidence, but here it looks like they have made up their mind already (but of course, the whole letter a scare-tactic to get fellow crazy conservative fundies to donate to Human Events, so, as with all advertising, anything goes as long as it sells.)

Amusingly, signed by Gary Kreep.

P. S.: This is the biggest political cover-up in American history! It would be so simple to release the documents to PROVE that Barack Obama is a natural-born citizen... IF HE HAD THE DOCUMENTS!

America has never before faced such a threat. Everything we hold dear is at risk with Barack Obama sitting as President without him releasing his actual birth certificate and other documents.

Barack Hussein Obama thinks he can get away with DUPING the American people and DESTROYING the U.S. Constitution. DON'T LET HIM DO IT! Please, make your best possible contribution to USJF today:

A few years ago I read John by Cynthia Lennon (2006), and it was quite an eye-opener for me. John and Cynthia were very happy together until two things happened much at the same time: LSD and Yoko Ono. Both changed John in major ways. From that point on, Cynthia was unable to connect to John, and they went their separate ways. For all the good things that happened as a consequence of that, including Sean, the music, the love, there is also a grim side to the story. John was never much of a father to Julian, who now was really pushed aside. On top of that, Cynthia had a very rough time financially, which stems from the fact that John contributed basically nothing to her and Julian.

And that I find disgraceful. John, I love your music, your lyrics, and your message. I love your fun-loving personality, your intelligence, and your depth. But I hate the way you treated your first wife and your first son. As much as I can weep at your love songs, I decry your choice to estrange them.

While my own two boys were busy in Borders reading about dinosaurs and Brown bear, brown bear, what do you see?, I picked up a children's biographical novel about Einstein. I learned some details about his life that had escaped me when I studied physics (it wasn't actually part of the curriculum).

In 1919, Einstein divorced from his first wife, Mileva, and quickly married his cousin, Elsa. Einstein wasn't financially well off in those days, and the divorce didn't make things better for Mileva. He did still support her and their two sons, but time were nonetheless rough on them. Having been nominated for the Nobel-prize three of four times at that point, Einstein promised Mileva that he would give her all the money that came with the prize when he should get it.

And here my heart skipped a beat, or however the idiom goes. I immediately drew the parallel to John Lennon. Both are persons that I look up to in terms of their work, and it is perhaps my weakness that I couple that with their personality (though I suspect that is a very common occurrence in many people, no?). So reading thus far I feared that Einstein wouldn't come through for his ex, just like Lennon (and just like Stephen Hawking, by the way, who got rich on A Brief History of Time, divorced his wife and married his nurse, and left his ex and children with next to no money).

Einstein was indeed awarded the 1921 Nobel prize in physics, neither for the special nor the general theory of relativity, but for the discovery of the photoelectric effect. Einstein collected the prize money in 1922, and then what did he do? He gave it all to Mileva as promised.

For that I thank you, Einstein. Thank you for that. You really made my day, more than 54 years later.

Update minutes after posting:

Well, wouldn't you know it. Look what it says on Wikipedia's page about Einstein:

It was long reported that Einstein gave the Nobel prize money directly to his first wife, Mileva Marić, in compliance with their 1919 divorce settlement. However, personal correspondence made public in 2006[121] shows that he invested much of it in the United States, and saw much of it wiped out in the Great Depression.

Compared to the sun that sits in the sky,compared to the clouds as they roll by,compared to the bugs and the spiders and flies,I am an ape man

Here's an excellent live recording of it from 1970.

Please notice the most wonderful young people brought in from the street. They are most uncool, which is something I value a lot. It was before my time, but I guess it was very much part of that time. The same phenomenon can be seen to an even greater extent in this live recording of Starman (another part-time favorite of mine).

The dancers merely sort of swing their arms a bit and otherwise stand on the same spot enjoying being on the scene. Precious.

This is a fantastic idea! Photoshopping pictures of models is apparently more common than I thought, and now a British politician is suggesting to prohibit the practice in advertisement targeting those under 16, and to require warning labels on all others (which could be just a credit stating who did the airbrushing).

Liberal Democrat MP Jo Swinson said the practice of altering pictures can harm young people's health and self-esteem and that “women are pressurised to conform to a narrow image of beauty".

Here is an in favor but sorely pessimistic view, saying that such a law will never pass. Nonsense, says I. If warning labels on cigarettes can be done, then why not this? It's not like it's going to hurt any political candidates financially. Or ideologically.

Just take a look at Kim Kardashian before and after airbrushing:

If children grow up thinking they have to look like Kim on the right when she herself looks like the one on the left, then I do think we owe it to them to tell them the truth.

There's also the problem of the moving pictures (films, premieres, award-shows) where the stars improve their looks with titty-tape and other tricks to look hot in the haute. How about public or private demonstrations of how this is done? Children/adolescents ought to know about this phenomenon just the same, so they don't get the false impression that this is how people really look, every day.

It's almost a duty to guide people to the reports about the atheist hordes' visit to Ken Ham's Creation Museum in Kentucky. The big news is that a Derek Rodgers was treated to an escort to the exit because he was wearing a t-shirt with the words "There’s Probably No God. Now Stop Worrying and Enjoy Your Life." Talk about offensive!

If you want to see just how exceptionally stupid some creationists are, read this article by the Atlanta Church and Culture Examiner, Genetics: science against evolution. You could write a whole treatise about the surplus of misconceptions, falsehoods, and illogical claims seen here. For example:

Microevolution is simply the rearranging of genetic information that is already present. A child may be born with blond, brown, red, or black hair. Hair could be curly, straight or a combination of the two. However, hair is still hair and no new information has been added to the genes.

This guy seriously does not understand the concept of information. If the parents have black hair and the offspring have red (and this is due to a mutation), then there is new information in the genome, namely to make the hair red. Exceptional asininanity.

The common claim that mutations can only cause loss of information, not increase information, can readily be dismembered:

Suppose a mutation changing Adenine to Guanine at a certain location in a gene causes a loss of information (it could destroy the whole gene by disrupting expression, for example), then - obviously - a mutation changing Guanine to Adenine in that same location causes results in a gain of information (the gene now functions again). Case closed.

If you then claim that humans are perfect, and thus every nucleotide is the optimal one from the beginning (that would be Genesis I), then the answer would be that when the environment changes (for example to suddenly include predators of humans), then there is no information in the genome about how to respond, and this can now be written into the genome by mutations. Whenever the environment changes, information is lost, and then mutations (in the very broad sense that includes SNPs, recombination, insertions, deletions, transposable elements, gene flow, horizontal transfer, etc.) is the way information is gained.

Baby Be-Bop the book is, in the words of author Francesca Lia Block, "a very sweet, simple, coming-of-age story about a young man's discovery that he's gay." A copy of it in the local library wouldn't normally obset anyone, except in this case the library is in West Bend, Wisconsin (to the coasters better known as "the middle of nowhere"). Then it's a major problem.

Read on Salon how, after the library board unanimously voted to leave this and other books where they are, despite protestations from the West Bend Citizens for Safe Libraries (*chortle* You'd think they'd be worried about terrorists bombing the library. I mean, with bombs), another group of outraged citizens took over the operation.

But the controversy isn't over. Now an outfit called the Christian Civil Liberties Union has gotten in on the act, suing the library for, according to the West Bend Daily News, "damaging" the "mental and emotional well-being" of several individuals by displaying "Baby Be-Bop" in the library. Since attempts to label the novel as "pornographic" have failed, the (somewhat shadowy) CCLU hopes to brand it as hate speech, in part because it contains the word "nigger." The complainants, described as "elderly" by the newspaper, claim that Block's novel is "explicitly vulgar, racial [sic] and anti-Christian." They want the library's copy not only removed but publicly burned.

What a mob of pathetic losers. One thing is calling themselves anything with 'civil liberties union' - people like these consistently abhor the ACLU. Another is that they insist on a real-life public book burning. Have these people read no history at all?

Dirk [book's main character] is beaten by gay bashers but steadfastly clings to the possibility of finding love.

I trust little Baby Be-Bop will prevail in the same manner in Wisconsin. I predict tolerance will defeat homophobia the same way in the end, though in America it looks very much like it means waiting for the conservative, Christian, elderly, zealots to die out.

If Wisconsinites don't stand up and boo their Christian retirees with nothing better to do than imitating Nazis, then I fear it'll be quite a while before Wisconsin becomes somewhere.

"Hmm... for some people, I hope so for them. For the people who believe in it, I hope so. There doesn't need to be a God for me. There's something in people that's spiritual, that's godlike. I don't feel like doing things just because people say things, but I also don't really know if it's better not to believe in anything either."

Math nerds (yes, there are different kinds) are making the big money. Stat nerds, actually. Right out of college. But the real treat in this blurby article, Math Nerds Getting Richer, Sexier, is the comments:

For example:

BL's one date with statistician:Math Boy (geeky but v. cute and in that big hands/wide pelvis way that usually means something good is afoot) rambles on and on about what he does, drops mathy science, for about an hour until BL's eyes are about to roll.BL: So what's the probability of your having a big cock, statistically (slurred) speaking?Math Boy: That would be fifty-fifty. Here, let me improve those odds. Bartender!That smart-looking lady in front of the blackboard who wrote that math is fun? She doesn't lie.

Cue the fitness landscape. A multi-dimensional function for organism fitness (ability to reproduce) as a function of the genotype*. A population moves "uphill" when it can to maximize fitness, akin to physical systems, which always moves to minimize its energy.

If the population (average) sits on the red dot in this fitness landscape (where fitness is on the ordinate (y-axis) and genotype is on the abscissa (x-axis)), then it will move up to the top of the peak (green dot), by spawning and acquiring beneficial mutations in a straight-forward manner.

Imagine, then, a landscape with many hills and valleys. Specifically, many peaks (local fitness optima) which, once 'inhabited', the population can only move away from by decreasing its fitness (moving from the green to the purple dot in the figure above). The individuals who do move away from the peak will have lower fitness, and thus won't have as many offspring (on average) as those who stay on the peak. Two or more genotypic mutations are required before the organisms can escape that local peak and ascend the adjacent higher one. When this happens, those individuals who stay behind will be outcompeted by the mutational emigrants.

But, since finding a new higher peak then requires that the organisms first decrease in fitness, then the question begs if this ever happens. It sounds like a very unlikely event, and, indeed, Darwin expressed concern about the matter:

"If it could be demonstrated that any complex organ existed, which could not possibly have been formed by numerous, successive, slight modifications, my theory would absolutely break down."

I am aware that Darwin most likely wasn't talking about decreasing fitness, but other have since taken it to mean that every genotypic change must be advantageous.

But there is now plenty of evidence that evolution doesn't (can't) always proceed by small steps that increase fitness, so...

the conventional assumption is that adaptation is far more likely to occur by single mutations which each increase the fitness, since double mutations or more complex processes are far less probable.

These two figures here of one-dimensional fitness landscapes illustrate this point. In figure a and b above, the population sits on a peak and needs two and three mutations to higher fitness, respectively. It is obviously easier to go straight up a hill, increasing fitness by every mutation, than these two situations, where the first one or two mutations will still not increase fitness, but a second or third mutation will. The question is how likely it is valleys like these can be crossed, and which parameters make it more likely.

This is answered by calculating the waiting times for a beneficial mutation (increasing fitness) to go to fixation (i.e. being present in all individuals, which, for asexuals populations, means that the individual that first acquired the mutation is an ancestor of all individuals at a later time). This time is denoted by τ:

The crosses are results from their simulations, and the lines are the analytically derived results (and they agree very well, don't you think?). The effect we see is that the larger the population size, the higher the mutation rate and the lower the fitness cost of the intermediate, deleterious mutations are, the less time it takes a population to cross a fitness-valley. This is not surprising: the larger the population is, the more mutations is tried per time, since more individuals means more offspring, and that offspring can mutate when the parent DNA is copied. And, of course, the higher the rate of mutation is, the more mutations. Lastly, the shallower the fitness-valley that must be crossed is, the more likely it is that the one- or two-mutant genotypes will produce offspring (which is required to generate a second/third mutant).

The phenomenon that gives rise to multiple peaks in the fitness-landscape is called epistasis: interaction between genes or between mutations. The first mutation alone decreases fitness. The second mutation alone (i.e. without the first one happening) is also deleterious. But together they are beneficial. This is termed positive epistasis, when the fitness of the two mutations together is higher than the sum (or product) of the fitness of the two mutations independently of each other.

Darwin's worries were unfounded. Yes, it's comfortable to imagine that evolution proceeds by ever so many slightly beneficial steps, but the fact that it doesn't always do that does not mean that Darwin's theory breaks down. At least not the way the Theory of Evolution is understood in this century.

* The fitness landscape really should be fitness as a function of the phenotype (all the physical characteristics of the organism), but in many computational models of evolutionary processes, the genotype (the genetic make-up) maps uniquely onto the phenotype, so there's no distinction.

Pleiotropy comes from the Greek πλείων pleion, meaning "more", and τρέπειν trepein, meaning "to turn, to convert". It designates the occurrence of a single gene affecting multiple traits, and is a hugely important concept in evolutionary biology.

I'm a postdoc at UC Santa Barbara.

All Many aspects of evolution interest me, but my research focus is currently on microbial evolution, adaptive radiation, speciation, fitness landscapes, epistasis, and the influence of genetic architecture on adaptation and speciation.